19-Mar-2020 Dear Loes, Peter, Clemens & Gerard, I concur that it is crucial to preserve the original diffraction data and make it available to anyone who would like to use it. As an example, please see the very recent paper by Nachon et al (2020). "A second look at the crystal structures of Drosophila melanogaster acetylcholinesterase in complex with tacrine derivatives provides Insights concerning catalytic intermediates and the design of specific insecticides" Molecules 25 pii: E1198 [https://www.ncbi.nlm.nih.gov/pubmed/32155891]. The study reexamines the original data, with modern software tools, the original data of a paper we published in 2000 (~20 years ago) and revealed features that had not been noticed. Specifically 1) previously unmodeled density in the native active site can be interpreted as stable acetylation of the catalytic serine. 2) Similarly, a strong density in the DmAChE/ZA complex, originally attributed to a sulfate ion, is better interpreted as a small molecule that is covalently bound. The complex is reminiscent of the carboxylate/BChE complexes observed in crystal structures of hBChE [Brazzolotto et al, 2012; Nicolet et al, 2003], and demonstrates the remarkable ability of ChEs to stabilize covalent complexes with carboxylates. Thus, the study demonstrates that updated processing of older diffraction images, and the re-refinement of older diffraction data, can produce valuable information that could not be detected in the original analysis, and strongly supports the preservation of the diffraction images in public data banks. Best regards Joel ------------------------------------------------------------------------------------ Prof. Joel L. Sussman. joel.suss...@weizmann.ac.il<mailto:joel.suss...@weizmann.ac.il> www.weizmann.ac.il/~joel<http://www.weizmann.ac.il/~joel> Dept. of Structural Biology tel: +972 (8) 934 6309 proteopedia.org<http://proteopedia.org> Weizmann Institute of Science fax: +972 (8) 934 6312 Rehovot 76100 ISRAEL mob: +972 (50) 510 9600 -------------------------------------------------------------------------------------
On 19 Mar 2020, at 11:32, Kroon-Batenburg, L.M.J. (Loes) <l.m.j.kroon-batenb...@uu.nl<mailto:l.m.j.kroon-batenb...@uu.nl>> wrote: Dear Gerard, This is a great idea. Of course I am very much in favour of making available raw diffraction images, and such a virtual workshop could demonstrate the usefulness of reprocessing raw diffraction data and structural refinements. I am not at all afraid that archiving of raw data that are the basis of a scientific paper will have significant environmental effects: this is minor compared to our everyday use of cloud services. And as Graeme mentioned: when archiving raw data make sure to add sufficient and correct meta data. Best wishes, Loes ___________________________________________________________ Dr. Loes Kroon-Batenburg Dept. of Crystal and Structural Chemistry Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8, 3584 CH Utrecht The Netherlands E-mail : l.m.j.kroon-batenb...@uu.nl<mailto:l.m.j.kroon-batenb...@uu.nl> phone : +31-30-2532865 fax : +31-30-2533940 ________________________________ Van: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>> namens Gerard Bricogne <g...@globalphasing.com<mailto:g...@globalphasing.com>> Verzonden: woensdag 18 maart 2020 23:30 Aan: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> <CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>> Onderwerp: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures Dear colleagues, Perusal and some initial (re-)refinement of the various SARS-CoV-2 protease structures in the PDB seems to indicate that that there might be potential to improve these if refinements could be repeated after some reprocessing and further analysis of the raw diffraction images, rather than against the deposited merged data. This statement should in no way be construed as a criticism of the remarkable achievements of the research groups concerned, who have been operating under tremendous time pressure, but as an exciting opportunity to push methods to their limits on a uniquely significant class of structures. Another consideration is that the various logistical problems created by COVID-19 may soon make it increasingly difficult to collect new diffraction data on potential drug targets relevant to the fight against SARS-CoV-2, underlining the importance of ensuring that the best results be obtained from every dataset actually collected, and that the most useful conclusions be drawn from the analysis of those datasets towards improving the quality of subsequent data collections. On this basis we would like to propose that special efforts be made to grant public access to the raw image data associated with any SARS-CoV-2 related structure that is deposited into the PDB. This can be done by (1) archiving these raw image data using resources such as data.sbgrid.org<http://data.sbgrid.org/>, zenodo.org<http://zenodo.org/>, proteindiffraction.org<http://proteindiffraction.org/> or any other cloud-based data-sharing service, and (2) communicating the corresponding DOIs to the wwPDB centres. This idea could be extended to datasets that investigators would like to offer to interested methods developers or expert users at the pre-deposition stage. Experts making use of those raw data would be encouraged to document, in as much detail as possible, how particular programs or workflows could be used on those structures/datasets to obtain the best results. This would be a kind of "virtual workshop", a particularly valuable collective activity at the present time when several in-person workshops (e.g. RapiData) have been cancelled and many meetings are in limbo for several months. The latter activity would benefit from having a centralised facility set up for the experts to post their results and annotations: we could create such a facility, but other, larger groups might want to consider doing so. With best wishes, Clemens & Gerard. ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
